3-12807306-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001162499.2(CAND2):c.213C>T(p.Cys71Cys) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000542 in 1,551,068 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001162499.2 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAND2 | NM_001162499.2 | c.213C>T | p.Cys71Cys | splice_region_variant, synonymous_variant | Exon 3 of 15 | ENST00000456430.6 | NP_001155971.1 | |
CAND2 | XM_011533504.3 | c.141C>T | p.Cys47Cys | splice_region_variant, synonymous_variant | Exon 3 of 15 | XP_011531806.1 | ||
CAND2 | XM_011533503.3 | c.213C>T | p.Cys71Cys | splice_region_variant, synonymous_variant | Exon 3 of 14 | XP_011531805.1 | ||
CAND2 | NM_012298.3 | c.213-2753C>T | intron_variant | Intron 2 of 12 | NP_036430.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152146Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000128 AC: 20AN: 155690Hom.: 0 AF XY: 0.000133 AC XY: 11AN XY: 82474
GnomAD4 exome AF: 0.0000565 AC: 79AN: 1398922Hom.: 0 Cov.: 29 AF XY: 0.0000507 AC XY: 35AN XY: 689940
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152146Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74326
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at